1
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Al-Fadhli AH, Jamal WY. Recent advances in gene-editing approaches for tackling antibiotic resistance threats: a review. Front Cell Infect Microbiol 2024; 14:1410115. [PMID: 38994001 PMCID: PMC11238145 DOI: 10.3389/fcimb.2024.1410115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/11/2024] [Indexed: 07/13/2024] Open
Abstract
Antibiotic resistance, a known global health challenge, involves the flow of bacteria and their genes among animals, humans, and their surrounding environment. It occurs when bacteria evolve and become less responsive to the drugs designated to kill them, making infections harder to treat. Despite several obstacles preventing the spread of genes and bacteria, pathogens regularly acquire novel resistance factors from other species, which reduces their ability to prevent and treat such bacterial infections. This issue requires coordinated efforts in healthcare, research, and public awareness to address its impact on human health worldwide. This review outlines how recent advances in gene editing technology, especially CRISPR/Cas9, unveil a breakthrough in combating antibiotic resistance. Our focus will remain on the relationship between CRISPR/cas9 and its impact on antibiotic resistance and its related infections. Moreover, the prospects of this new advanced research and the challenges of adopting these technologies against infections will be outlined by exploring its different derivatives and discussing their advantages and limitations over others, thereby providing a corresponding reference for the control and prevention of the spread of antibiotic resistance.
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Affiliation(s)
- Amani H Al-Fadhli
- Laboratory Sciences, Department of Medical, Faculty of Allied Health Sciences, Health Sciences Center (HSC), Kuwait University, Jabriya, Kuwait
| | - Wafaa Yousef Jamal
- Department of Microbiology, College of Medicine, Kuwait University, Jabriya, Kuwait
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2
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Stege PB, Beekman JM, Hendrickx APA, van Eijk L, Rogers MRC, Suen SWF, Vonk AM, Willems RJL, Paganelli FL. Colonization of vancomycin-resistant Enterococcus faecium in human-derived colonic epithelium: unraveling the transcriptional dynamics of host-enterococcal interactions. FEMS MICROBES 2024; 5:xtae014. [PMID: 38813098 PMCID: PMC11134301 DOI: 10.1093/femsmc/xtae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/27/2024] [Accepted: 05/06/2024] [Indexed: 05/31/2024] Open
Abstract
Enterococcus faecium is an opportunistic pathogen able to colonize the intestines of hospitalized patients. This initial colonization is an important step in the downstream pathogenesis, which includes outgrowth of the intestinal microbiota and potential infection of the host. The impact of intestinal overgrowth on host-enterococcal interactions is not well understood. We therefore applied a RNAseq approach in order to unravel the transcriptional dynamics of E. faecium upon co-culturing with human derived colonic epithelium. Co-cultures of colonic epithelium with a hospital-associated vancomycin resistant (vanA-type) E. faecium (VRE) showed that VRE resided on top of the colonic epithelium when analyzed by microscopy. RNAseq revealed that exposure to the colonic epithelium resulted in upregulation of 238 VRE genes compared to the control condition, including genes implicated in pili expression, conjugation (plasmid_2), genes related to sugar uptake, and biofilm formation (chromosome). In total, 260 were downregulated, including the vanA operon located on plasmid_3. Pathway analysis revealed an overall switch in metabolism to amino acid scavenging and reduction. In summary, our study demonstrates that co-culturing of VRE with human colonic epithelium promotes an elaborate gene response in VRE, enhancing our insight in host-E. faecium interactions, which might facilitate the design of novel anti-infectivity strategies.
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Affiliation(s)
- Paul B Stege
- Department of Medical Microbiology, UMC Utrecht, Utrecht, 3584CX, The Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, 3584CX, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, 3584CX, The Netherlands
| | - Antoni P A Hendrickx
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721MA, The Netherlands
| | - Laura van Eijk
- Department of Medical Microbiology, UMC Utrecht, Utrecht, 3584CX, The Netherlands
| | - Malbert R C Rogers
- Department of Medical Microbiology, UMC Utrecht, Utrecht, 3584CX, The Netherlands
| | - Sylvia W F Suen
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, 3584CX, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, 3584CX, The Netherlands
| | - Annelotte M Vonk
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, 3584CX, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, 3584CX, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, UMC Utrecht, Utrecht, 3584CX, The Netherlands
| | - Fernanda L Paganelli
- Department of Medical Microbiology, UMC Utrecht, Utrecht, 3584CX, The Netherlands
- Winclove Probiotics, Amsterdam, 1033JS, The Netherlands
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3
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Allemailem KS. Recent Advances in Understanding the Molecular Mechanisms of Multidrug Resistance and Novel Approaches of CRISPR/Cas9-Based Genome-Editing to Combat This Health Emergency. Int J Nanomedicine 2024; 19:1125-1143. [PMID: 38344439 PMCID: PMC10859101 DOI: 10.2147/ijn.s453566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
The rapid spread of multidrug resistance (MDR), due to abusive use of antibiotics has led to global health emergency, causing substantial morbidity and mortality. Bacteria attain MDR by different means such as antibiotic modification/degradation, target protection/modification/bypass, and enhanced efflux mechanisms. The classical approaches of counteracting MDR bacteria are expensive and time-consuming, thus, it is highly significant to understand the molecular mechanisms of this resistance to curb the problem from core level. The revolutionary approach of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated sequence 9 (CRISPR/Cas9), considered as a next-generation genome-editing tool presents an innovative opportunity to precisely target and edit bacterial genome to alter their MDR strategy. Different bacteria possessing antibiotic resistance genes such as mecA, ermB, ramR, tetA, mqrB and blaKPC that have been targeted by CRISPR/Cas9 to re-sensitize these pathogens against antibiotics, such as methicillin, erythromycin, tigecycline, colistin and carbapenem, respectively. The CRISPR/Cas9 from S. pyogenes is the most widely studied genome-editing tool, consisting of a Cas9 DNA endonuclease associated with tracrRNA and crRNA, which can be systematically coupled as sgRNA. The targeting strategies of CRISPR/Cas9 to bacterial cells is mediated through phage, plasmids, vesicles and nanoparticles. However, the targeting approaches of this genome-editing tool to specific bacteria is a challenging task and still remains at a very preliminary stage due to numerous obstacles awaiting to be solved. This review elaborates some recent updates about the molecular mechanisms of antibiotic resistance and the innovative role of CRISPR/Cas9 system in modulating these resistance mechanisms. Furthermore, the delivery approaches of this genome-editing system in bacterial cells are discussed. In addition, some challenges and future prospects are also described.
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Affiliation(s)
- Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah51452, Saudi Arabia
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4
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Deb R, Chaudhary P, De S. CRISPR/cas9 cassette targeting Escherichia coli blaCTX-M specific gene of mastitis cow milk origin can alter the antibiotic resistant phenotype for cefotaxime. Anim Biotechnol 2023; 34:1849-1854. [PMID: 35357269 DOI: 10.1080/10495398.2022.2053695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
CTX-M beta-lactamases are one of the most important extended spectrum beta-lactamase (ESBL) resistance enzymes found in E. coli. In the present study, 59% of E. coli isolates from mastitis cow milk were reported to be positive for ESBL types. The prevalence of beta-lactam (β-lactam) antibiotic resistance was reported to be 84%, 72.7%, 52.27%, 50%, and 45.4% for cefotaxime, cefepime, cefuroxime, oxacillin, and cephalexine, respectively. The blaCTX-M gene was found in 65% (n = 17) of the E. coli isolates when they were genotyped. Further, the use of a CRISPR/cas9 cassette to target the E. coli blaCTX-M gene revealed changes in antibiotic phenotypes for cefotaxime.
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Affiliation(s)
- Rajib Deb
- Animal Genomics Laboratory, Animal Biotechnology Center, ICAR-National Dairy Research Institute, Karnal, India
- ICAR-National Research Center on Pig, Guwahati, Assam, India
| | - Parul Chaudhary
- Animal Genomics Laboratory, Animal Biotechnology Center, ICAR-National Dairy Research Institute, Karnal, India
| | - Sachinandan De
- Animal Genomics Laboratory, Animal Biotechnology Center, ICAR-National Dairy Research Institute, Karnal, India
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5
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Rabaan AA, Al Fares MA, Almaghaslah M, Alpakistany T, Al Kaabi NA, Alshamrani SA, Alshehri AA, Almazni IA, Saif A, Hakami AR, Khamis F, Alfaresi M, Alsalem Z, Alsoliabi ZA, Al Amri KAS, Hassoueh AK, Mohapatra RK, Arteaga-Livias K, Alissa M. Application of CRISPR-Cas System to Mitigate Superbug Infections. Microorganisms 2023; 11:2404. [PMID: 37894063 PMCID: PMC10609045 DOI: 10.3390/microorganisms11102404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
Multidrug resistance in bacterial strains known as superbugs is estimated to cause fatal infections worldwide. Migration and urbanization have resulted in overcrowding and inadequate sanitation, contributing to a high risk of superbug infections within and between different communities. The CRISPR-Cas system, mainly type II, has been projected as a robust tool to precisely edit drug-resistant bacterial genomes to combat antibiotic-resistant bacterial strains effectively. To entirely opt for its potential, advanced development in the CRISPR-Cas system is needed to reduce toxicity and promote efficacy in gene-editing applications. This might involve base-editing techniques used to produce point mutations. These methods employ designed Cas9 variations, such as the adenine base editor (ABE) and the cytidine base editor (CBE), to directly edit single base pairs without causing DSBs. The CBE and ABE could change a target base pair into a different one (for example, G-C to A-T or C-G to A-T). In this review, we addressed the limitations of the CRISPR/Cas system and explored strategies for circumventing these limitations by applying diverse base-editing techniques. Furthermore, we also discussed recent research showcasing the ability of base editors to eliminate drug-resistant microbes.
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Affiliation(s)
- Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Mona A. Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah 21589, Saudi Arabia
| | - Manar Almaghaslah
- Infectious Disease Division, Department of Internal Medicine, Dammam Medical Complex, Dammam 32245, Saudi Arabia
| | - Tariq Alpakistany
- Bacteriology Department, Public Health Laboratory, Taif 26521, Saudi Arabia
| | - Nawal A. Al Kaabi
- College of Medicine and Health Science, Khalifa University, Abu Dhabi 127788, United Arab Emirates
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi 51900, United Arab Emirates
| | - Saleh A. Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Ahmad A. Alshehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Ibrahim Abdullah Almazni
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Ahmed Saif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 62223, Saudi Arabia
| | - Abdulrahim R. Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 62223, Saudi Arabia
| | - Faryal Khamis
- Infection Diseases Unit, Department of Internal Medicine, Royal Hospital, Muscat 1331, Oman
| | - Mubarak Alfaresi
- Department of Pathology and Laboratory Medicine, Zayed Military Hospital, Abu Dhabi 3740, United Arab Emirates
- Department of Pathology, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates
| | - Zainab Alsalem
- Department of Epidemic Diseases Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | | | | | - Amal K. Hassoueh
- Pharmacy Department, King Saud Medical City, Riyadh 7790, Saudi Arabia
| | - Ranjan K. Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar 758002, India
| | - Kovy Arteaga-Livias
- Escuela de Medicina-Filial Ica, Universidad Privada San Juan Bautista, Ica 11000, Peru
- Escuela de Medicina, Universidad Nacional Hermilio Valdizán, Huanuco 10000, Peru
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
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6
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Qian Y, Zhou D, Li M, Zhao Y, Liu H, Yang L, Ying Z, Huang G. Application of CRISPR-Cas system in the diagnosis and therapy of ESKAPE infections. Front Cell Infect Microbiol 2023; 13:1223696. [PMID: 37662004 PMCID: PMC10470840 DOI: 10.3389/fcimb.2023.1223696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/24/2023] [Indexed: 09/05/2023] Open
Abstract
Antimicrobial-resistant ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. ESKAPE pathogens are the most common opportunistic pathogens in nosocomial infections, and a considerable number of their clinical isolates are not susceptible to conventional antimicrobial therapy. Therefore, innovative therapeutic strategies that can effectively deal with ESKAPE pathogens will bring huge social and economic benefits and ease the suffering of tens of thousands of patients. Among these strategies, CRISPR (clustered regularly interspaced short palindromic repeats) system has received extra attention due to its high specificity. Regrettably, there is currently no direct CRISPR-system-based anti-infective treatment. This paper reviews the applications of CRISPR-Cas system in the study of ESKAPE pathogens, aiming to provide directions for the research of ideal new drugs and provide a reference for solving a series of problems caused by multidrug-resistant bacteria (MDR) in the post-antibiotic era. However, most research is still far from clinical application.
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Affiliation(s)
- Yizheng Qian
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, China
| | - Dapeng Zhou
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, China
- Department of Burn Plastic and Wound Repair Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Min Li
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, China
| | - Yongxiang Zhao
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, China
| | - Huanhuan Liu
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, China
| | - Li Yang
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, China
| | - Zhiqin Ying
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, China
| | - Guangtao Huang
- Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, China
- Department of Burn and Plastic Surgery, Department of Wound Repair, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
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7
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Mayorga-Ramos A, Zúñiga-Miranda J, Carrera-Pacheco SE, Barba-Ostria C, Guamán LP. CRISPR-Cas-Based Antimicrobials: Design, Challenges, and Bacterial Mechanisms of Resistance. ACS Infect Dis 2023; 9:1283-1302. [PMID: 37347230 PMCID: PMC10353011 DOI: 10.1021/acsinfecdis.2c00649] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Indexed: 06/23/2023]
Abstract
The emergence of antibiotic-resistant bacterial strains is a source of public health concern across the globe. As the discovery of new conventional antibiotics has stalled significantly over the past decade, there is an urgency to develop novel approaches to address drug resistance in infectious diseases. The use of a CRISPR-Cas-based system for the precise elimination of targeted bacterial populations holds promise as an innovative approach for new antimicrobial agent design. The CRISPR-Cas targeting system is celebrated for its high versatility and specificity, offering an excellent opportunity to fight antibiotic resistance in pathogens by selectively inactivating genes involved in antibiotic resistance, biofilm formation, pathogenicity, virulence, or bacterial viability. The CRISPR-Cas strategy can enact antimicrobial effects by two approaches: inactivation of chromosomal genes or curing of plasmids encoding antibiotic resistance. In this Review, we provide an overview of the main CRISPR-Cas systems utilized for the creation of these antimicrobials, as well as highlighting promising studies in the field. We also offer a detailed discussion about the most commonly used mechanisms for CRISPR-Cas delivery: bacteriophages, nanoparticles, and conjugative plasmids. Lastly, we address possible mechanisms of interference that should be considered during the intelligent design of these novel approaches.
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Affiliation(s)
- Arianna Mayorga-Ramos
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
| | - Johana Zúñiga-Miranda
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
| | - Saskya E. Carrera-Pacheco
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
| | - Carlos Barba-Ostria
- Escuela
de Medicina, Colegio de Ciencias de la Salud Quito, Universidad San Francisco de Quito USFQ, Quito 170902, Ecuador
| | - Linda P. Guamán
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
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8
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Junaid M, Thirapanmethee K, Khuntayaporn P, Chomnawang MT. CRISPR-Based Gene Editing in Acinetobacter baumannii to Combat Antimicrobial Resistance. Pharmaceuticals (Basel) 2023; 16:920. [PMID: 37513832 PMCID: PMC10384873 DOI: 10.3390/ph16070920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial resistance (AMR) poses a significant threat to the health, social, environment, and economic sectors on a global scale and requires serious attention to addressing this issue. Acinetobacter baumannii was given top priority among infectious bacteria because of its extensive resistance to nearly all antibiotic classes and treatment options. Carbapenem-resistant A. baumannii is classified as one of the critical-priority pathogens on the World Health Organization (WHO) priority list of antibiotic-resistant bacteria for effective drug development. Although available genetic manipulation approaches are successful in A. baumannii laboratory strains, they are limited when employed on newly acquired clinical strains since such strains have higher levels of AMR than those used to select them for genetic manipulation. Recently, the CRISPR-Cas (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) system has emerged as one of the most effective, efficient, and precise methods of genome editing and offers target-specific gene editing of AMR genes in a specific bacterial strain. CRISPR-based genome editing has been successfully applied in various bacterial strains to combat AMR; however, this strategy has not yet been extensively explored in A. baumannii. This review provides detailed insight into the progress, current scenario, and future potential of CRISPR-Cas usage for AMR-related gene manipulation in A. baumannii.
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Affiliation(s)
- Muhammad Junaid
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Krit Thirapanmethee
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Piyatip Khuntayaporn
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Mullika Traidej Chomnawang
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
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9
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CRISPR in Modulating Antibiotic Resistance of ESKAPE Pathogens. Mol Biotechnol 2023; 65:1-16. [PMID: 35939207 DOI: 10.1007/s12033-022-00543-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 07/13/2022] [Indexed: 01/11/2023]
Abstract
The ESKAPE (Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) isolates both from the clinical settings and food products are demonstrated to gain resistance to multiple antimicrobials. Therefore, the ESKAPE pathogens pose a serious threat to public health, which warrants specific attention to developing alternative novel therapeutics. The clustered regularly interspaced short palindromic repeats associated (CRISPR-Cas) system is one of the novel methods for managing antibiotic-resistant strains. Specific Cas nucleases can be programmed against bacterial genomic sequences to decrease bacterial resistance to antibiotics. Moreover, a few CRISPR-Cas nucleases have the ability to the sequence-specific killing of bacterial strains. However, some pathogens acquire antibiotic resistance due to the presence of the CRISPR-Cas system. In brief, there is a wide range of functional diversity of CRISPR-Cas systems in bacterial pathogens. Hence, to be an effective and safe infection treatment strategy, a comprehensive understanding of the role of CRISPR-Cas systems in modulating antibiotic resistance in ESKAPE pathogens is essential. The present review summarizes all the mechanisms by which CRISPR confers and prevents antibiotic resistance in ESKAPE. The review also emphasizes the relationship between CRISPR-Cas systems, biofilm formation, and antibiotic resistance in ESKAPE.
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10
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Krause AL, Stinear TP, Monk IR. Barriers to genetic manipulation of Enterococci: Current Approaches and Future Directions. FEMS Microbiol Rev 2022; 46:6650352. [PMID: 35883217 PMCID: PMC9779914 DOI: 10.1093/femsre/fuac036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 01/09/2023] Open
Abstract
Enterococcus faecalis and Enterococcus faecium are Gram-positive commensal gut bacteria that can also cause fatal infections. To study clinically relevant multi-drug resistant E. faecalis and E. faecium strains, methods are needed to overcome physical (thick cell wall) and enzymatic barriers that limit the transfer of foreign DNA and thus prevent facile genetic manipulation. Enzymatic barriers to DNA uptake identified in E. faecalis and E. faecium include type I, II and IV restriction modification systems and CRISPR-Cas. This review examines E. faecalis and E. faecium DNA defence systems and the methods with potential to overcome these barriers. DNA defence system bypass will allow the application of innovative genetic techniques to expedite molecular-level understanding of these important, but somewhat neglected, pathogens.
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Affiliation(s)
- Alexandra L Krause
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC 3000 Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC 3000 Australia
| | - Ian R Monk
- Corresponding author: Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC 3000 Australia. E-mail:
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11
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Kurushima J, Tomita H. Advances of genetic engineering in Streptococci and Enterococci. Microbiol Immunol 2022; 66:411-417. [PMID: 35703039 DOI: 10.1111/1348-0421.13015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/09/2022] [Accepted: 06/11/2022] [Indexed: 11/26/2022]
Abstract
In the post-genome era, reverse genetic engineering is an indispensable methodology for experimental molecular biology to provide a deeper understanding of the principal relationship between genomic features and biological phenotypes. Technically, genetic engineering is carried out through allele replacement of a target genomic locus with a designed nucleotide sequence, so called site-directed mutagenesis. To artificially manipulate allele replacement through homologous recombination, researchers have improved various methodologies that are optimized to the bacterial species of interest. Here, we review widely used genetic engineering technologies, particularly for streptococci and enterococci, and recent advances that enable more effective and flexible manipulation. The development of genetic engineering has been promoted by synthetic biology approaches based on basic biology knowledge of horizontal gene transfer systems, such as natural conjugative transfer, natural transformation, and the CRISPR/Cas system. Therefore, this review also describes basic insights into molecular biology that underlie improvements in genetic engineering technology. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jun Kurushima
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22, Showa-machi, Maebashi-shi, Gunma, 371-8511, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22, Showa-machi, Maebashi-shi, Gunma, 371-8511, Japan.,Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, 3-39-22, Showa-machi, Maebashi-shi, Gunma, 371-8511, Japan
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12
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Han X, Zhou X, Pei Z, Stanton C, Ross RP, Zhao J, Zhang H, Yang B, Chen W. Characterization of CRISPR-Cas systems in Bifidobacterium breve. Microb Genom 2022; 8. [PMID: 35451949 PMCID: PMC9453068 DOI: 10.1099/mgen.0.000812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein (Cas) system is an important adaptive immune system for bacteria to resist foreign DNA infection, which has been widely used in genotyping and gene editing. To provide a theoretical basis for the application of the CRISPR-Cas system in Bifidobacterium breve, the occurrence and diversity of CRISPR-Cas systems were analysed in 150 B. breve strains. Specifically, 47 % (71/150) of B. breve genomes possessed the CRISPR-Cas system, and type I-C CRISPR-Cas system was the most widely distributed among those strains. The spacer sequences present in B. breve can be used as a genotyping marker. Additionally, the phage assembly-related proteins were important targets of the type I-C CRISPR-Cas system in B. breve, and the protospacer adjacent motif sequences were further characterized in B. breve type I-C system as 5'-TTC-3'. All these results might provide a molecular basis for the development of endogenous genome editing tools in B. breve.
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Affiliation(s)
- Xiao Han
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, PR China.,School of Food Science and Technology, Jiangnan University, Wuxi, PR China
| | - Xingya Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, PR China.,School of Food Science and Technology, Jiangnan University, Wuxi, PR China
| | - Zhangming Pei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, PR China.,School of Food Science and Technology, Jiangnan University, Wuxi, PR China
| | - Catherine Stanton
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, PR China.,APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Co., Cork, Ireland
| | - R Paul Ross
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, PR China.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, PR China.,School of Food Science and Technology, Jiangnan University, Wuxi, PR China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, PR China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, PR China.,School of Food Science and Technology, Jiangnan University, Wuxi, PR China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, PR China.,Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, PR China
| | - Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, PR China.,School of Food Science and Technology, Jiangnan University, Wuxi, PR China.,International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, PR China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, PR China.,School of Food Science and Technology, Jiangnan University, Wuxi, PR China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, PR China
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13
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Abstract
Considered a serious threat by the Centers for Disease Control and Prevention, multidrug-resistant Enterococcus faecium is an increasing cause of hospital-acquired infection. Here, we provide details on a single-plasmid CRISPR-Cas12a system for generating clean deletions and insertions. Single manipulations were carried out in under 2 weeks, with successful deletions/insertions present in >80% of the clones tested. Using this method, we generated three individual clean deletion mutations in the acpH, treA, and lacL genes and inserted codon-optimized unaG, enabling green fluorescent protein (GFP)-like fluorescence under the control of the trehalase operon. The use of in vivo recombination for plasmid construction kept costs to a minimum. IMPORTANCE Enterococcus faecium is increasingly associated with hard-to-treat antibiotic-resistant infections. The ability to generate clean genomic alterations is the first step in generating a complete mechanistic understanding of how E. faecium acquires pathogenic traits and causes disease. Here, we show that CRISPR-Cas12a can be used to quickly (under 2 weeks) and cheaply delete or insert genes into the E. faecium genome. This substantial improvement over current methods should speed up research on this important opportunistic pathogen.
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14
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Li Q, Zhang J, Yang J, Jiang Y, Yang S. Recent progress on n-butanol production by lactic acid bacteria. World J Microbiol Biotechnol 2021; 37:205. [PMID: 34698975 DOI: 10.1007/s11274-021-03173-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/13/2021] [Indexed: 11/26/2022]
Abstract
n-Butanol is an essential chemical intermediate produced through microbial fermentation. However, its toxicity to microbial cells has limited its production to a great extent. The anaerobe lactic acid bacteria (LAB) are the most resistant to n-butanol, so it should be the first choice for improving n-butanol production. The present article aims to review the following aspects of n-butanol production by LAB: (1) the tolerance of LAB to n-butanol, including its tolerance level and potential tolerance mechanisms; (2) genome editing tools in the n-butanol-resistant LAB; (3) methods of LAB modification for n-butanol production and the production levels after modification. This review will provide a theoretical basis for further research on n-butanol production by LAB.
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Affiliation(s)
- Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Jieze Zhang
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Junjie Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou, 313000, China
- Shanghai Taoyusheng Biotechnology Company Ltd, Shanghai, 200032, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou, 313000, China.
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15
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Johnson CN, Sheriff EK, Duerkop BA, Chatterjee A. Let Me Upgrade You: Impact of Mobile Genetic Elements on Enterococcal Adaptation and Evolution. J Bacteriol 2021; 203:e0017721. [PMID: 34370561 PMCID: PMC8508098 DOI: 10.1128/jb.00177-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococci are Gram-positive bacteria that have evolved to thrive as both commensals and pathogens, largely due to their accumulation of mobile genetic elements via horizontal gene transfer (HGT). Common agents of HGT include plasmids, transposable elements, and temperate bacteriophages. These vehicles of HGT have facilitated the evolution of the enterococci, specifically Enterococcus faecalis and Enterococcus faecium, into multidrug-resistant hospital-acquired pathogens. On the other hand, commensal strains of Enterococcus harbor CRISPR-Cas systems that prevent the acquisition of foreign DNA, restricting the accumulation of mobile genetic elements. In this review, we discuss enterococcal mobile genetic elements by highlighting their contributions to bacterial fitness, examine the impact of CRISPR-Cas on their acquisition, and identify key areas of research that can improve our understanding of enterococcal evolution and ecology.
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Affiliation(s)
- Cydney N. Johnson
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Emma K. Sheriff
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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16
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Chen V, Griffin ME, Maguin P, Varble A, Hang HC. RecT Recombinase Expression Enables Efficient Gene Editing in Enterococcus spp. Appl Environ Microbiol 2021; 87:e0084421. [PMID: 34232061 PMCID: PMC8388837 DOI: 10.1128/aem.00844-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/25/2021] [Indexed: 12/24/2022] Open
Abstract
Enterococcus faecium is a ubiquitous Gram-positive bacterium that has been recovered from the environment, food, and microbiota of mammals. Commensal strains of E. faecium can confer beneficial effects on host physiology and immunity, but antibiotic usage has afforded antibiotic-resistant and pathogenic isolates from livestock and humans. However, the dissection of E. faecium functions and mechanisms has been restricted by inefficient gene-editing methods. To address these limitations, here, we report that the expression of E. faecium RecT recombinase significantly improves the efficiency of recombineering technologies in both commensal and antibiotic-resistant strains of E. faecium and other Enterococcus species such as E. durans and E. hirae. Notably, the expression of RecT in combination with clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 and guide RNAs (gRNAs) enabled highly efficient scarless single-stranded DNA recombineering to generate specific gene-editing mutants in E. faecium. Moreover, we demonstrate that E. faecium RecT expression facilitated chromosomal insertions of double-stranded DNA templates encoding antibiotic-selectable markers to generate gene deletion mutants. As a further proof of principle, we use CRISPR-Cas9-mediated recombineering to knock out both sortase A genes in E. faecium for downstream functional characterization. The general RecT-mediated recombineering methods described here should significantly enhance genetic studies of E. faecium and other closely related species for functional and mechanistic studies. IMPORTANCE Enterococcus faecium is widely recognized as an emerging public health threat with the rise of drug resistance and nosocomial infections. Nevertheless, commensal Enterococcus strains possess beneficial health functions in mammals to upregulate host immunity and prevent microbial infections. This functional dichotomy of Enterococcus species and strains highlights the need for in-depth studies to discover and characterize the genetic components underlying its diverse activities. However, current genetic engineering methods in E. faecium still require passive homologous recombination from plasmid DNA. This involves the successful cloning of multiple homologous fragments into a plasmid, introducing the plasmid into E. faecium, and screening for double-crossover events that can collectively take up to multiple weeks to perform. To alleviate these challenges, we show that RecT recombinase enables the rapid and efficient integration of mutagenic DNA templates to generate substitutions, deletions, and insertions in the genomic DNA of E. faecium. These improved recombineering methods should facilitate functional and mechanistic studies of Enterococcus.
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Affiliation(s)
- Victor Chen
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York, USA
| | - Matthew E. Griffin
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York, USA
| | - Pascal Maguin
- Laboratory of Bacteriology, The Rockefeller University, New York, New York, USA
| | - Andrew Varble
- Laboratory of Bacteriology, The Rockefeller University, New York, New York, USA
| | - Howard C. Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York, USA
- Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA
- Department of Chemistry, Scripps Research, La Jolla, California, USA
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17
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CRISPR-Cas, a Revolution in the Treatment and Study of ESKAPE Infections: Pre-Clinical Studies. Antibiotics (Basel) 2021; 10:antibiotics10070756. [PMID: 34206474 PMCID: PMC8300728 DOI: 10.3390/antibiotics10070756] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/14/2022] Open
Abstract
One of the biggest threats we face globally is the emergence of antimicrobial-resistant (AMR) bacteria, which runs in parallel with the lack in the development of new antimicrobials. Among these AMR bacteria pathogens belonging to the ESKAPE group can be highlighted (Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) due to their profile of drug resistance and virulence. Therefore, innovative lines of treatment must be developed for these bacteria. In this review, we summarize the different strategies for the treatment and study of molecular mechanisms of AMR in the ESKAPE pathogens based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins’ technologies: loss of plasmid or cellular viability, random mutation or gene deletion as well directed mutations that lead to a gene’s loss of function.
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18
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Li N, Wang M, Yu S, Zhou J. Optimization of CRISPR-Cas9 through promoter replacement and efficient production of L-homoserine in Corynebacterium glutamicum. Biotechnol J 2021; 16:e2100093. [PMID: 34018325 DOI: 10.1002/biot.202100093] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/04/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Corynebacterium glutamicum is an important chassis for industrial applications. The low efficiency of commonly used genome editing methods for C. glutamicum limits the rapid multiple engineering of the bacterium. MAIN METHODS AND MAJOR RESULTS In this study, chromosome-borne expression of cas9 and recET from Escherichia coli K12-MG1655 was achieved to avoid toxicity to the strain, increase the probability of homologous recombination, and reduce loss of viability caused by double-strand breaks. Constitutive strong promoters, such as P45 , Ptrc , and PH36 , were used to replace PglyA and to expand the application of the CRISPR-Cas9 system. By using this system, a C. glutamicum strain producing L-homoserine to 22.1 g per L in a 5-L bioreactor after 96 h was obtained. CONCLUSIONS AND IMPLICATIONS Through the application of visualized fluorescent protein, the process of plasmid curing was optimized, obtain a continuous and rapid CRISPR-Cas9 genome editing system. The method described here could be useful to construct C. glutamicum mutant rapidly.
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Affiliation(s)
- Ning Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China.,State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Miao Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Shiqin Yu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
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19
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Synefiaridou D, Veening JW. Harnessing CRISPR-Cas9 for Genome Editing in Streptococcus pneumoniae D39V. Appl Environ Microbiol 2021; 87:e02762-20. [PMID: 33397704 PMCID: PMC8105017 DOI: 10.1128/aem.02762-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 12/21/2020] [Indexed: 11/20/2022] Open
Abstract
CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by the detection and cleavage of invading foreign DNA. Modified versions of this system can be exploited as a biotechnological tool for precise genome editing at a targeted locus. Here, we developed a replicative plasmid that carries the CRISPR-Cas9 system for RNA-programmable genome editing by counterselection in the opportunistic human pathogen Streptococcus pneumoniae Specifically, we demonstrate an approach for making targeted markerless gene knockouts and large genome deletions. After a precise double-stranded break (DSB) is introduced, the cells' DNA repair mechanism of homology-directed repair (HDR) is exploited to select successful transformants. This is achieved through the transformation of a template DNA fragment that will recombine in the genome and eliminate recognition of the target of the Cas9 endonuclease. Next, the newly engineered strain can be easily cured from the plasmid, which is temperature sensitive for replication, by growing it at the nonpermissive temperature. This allows for consecutive rounds of genome editing. Using this system, we engineered a strain with three major virulence factors deleted. The approaches developed here could potentially be adapted for use with other Gram-positive bacteria.IMPORTANCEStreptococcus pneumoniae (the pneumococcus) is an important opportunistic human pathogen killing more than 1 million people each year. Having the availability of a system capable of easy genome editing would significantly facilitate drug discovery and efforts to identify new vaccine candidates. Here, we introduced an easy-to-use system to perform multiple rounds of genome editing in the pneumococcus by putting the CRISPR-Cas9 system on a temperature-sensitive replicative plasmid. The approaches used here will advance genome editing projects in this important human pathogen.
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Affiliation(s)
- Dimitra Synefiaridou
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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20
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de Maat V, Arredondo-Alonso S, Willems RJL, van Schaik W. Conditionally essential genes for survival during starvation in Enterococcus faecium E745. BMC Genomics 2020; 21:568. [PMID: 32811437 PMCID: PMC7437932 DOI: 10.1186/s12864-020-06984-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/12/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The nosocomial pathogen Enterococcus faecium can survive for prolonged periods of time on surfaces in the absence of nutrients. This trait is thought to contribute to the ability of E. faecium to spread among patients in hospitals. There is currently a lack of data on the mechanisms that are responsible for the ability of E. faecium to survive in the absence of nutrients. RESULTS We performed a high-throughput transposon mutant library screening (Tn-seq) to identify genes that have a role in long-term survival during incubation in phosphate-buffered saline (PBS) at 20 °C. A total of 24 genes were identified by Tn-seq to contribute to survival in PBS, with functions associated with the general stress response, DNA repair, metabolism, and membrane homeostasis. The gene which was quantitatively most important for survival in PBS was usp (locus tag: EfmE745_02439), which is predicted to encode a 17.4 kDa universal stress protein. After generating a targeted deletion mutant in usp, we were able to confirm that usp significantly contributes to survival in PBS and this defect was restored by in trans complementation. The usp gene is present in 99% of a set of 1644 E. faecium genomes that collectively span the diversity of the species. CONCLUSIONS We postulate that usp is a key determinant for the remarkable environmental robustness of E. faecium. Further mechanistic studies into usp and other genes identified in this study may shed further light on the mechanisms by which E. faecium can survive in the absence of nutrients for prolonged periods of time.
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Affiliation(s)
- Vincent de Maat
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Sergio Arredondo-Alonso
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands. .,Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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21
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Ferrera-Suanzes M, Prieto V, Medina-Olivera AJ, Botubol-Ares JM, Galán-Sánchez F, Rodríguez-Iglesias MA, Hernández-Galán R, Durán-Peña MJ. Synthesis of Degraded Limonoid Analogs as New Antibacterial Scaffolds against Staphylococcus aureus. Antibiotics (Basel) 2020; 9:antibiotics9080488. [PMID: 32781770 PMCID: PMC7459938 DOI: 10.3390/antibiotics9080488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/26/2020] [Accepted: 08/04/2020] [Indexed: 12/21/2022] Open
Abstract
Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA) have become serious infections in humans and ruminants. S. aureus strains are showing rapid changes to develop resistance in traditional antibiotic-containing systems. In the continuous fierce fight against the emergent multi-drug resistant bacterial strains, straightforward and scalable synthetic procedures to produce new active molecules are in demand. Analysis of molecular properties points to degraded limonoids as promising candidates. In this article, we report a simple synthetic approach to obtain degraded limonoid analogs as scaffolds for new antibacterial molecules. The minimum inhibitory concentrations against S. aureus were evaluated for the stereoisomer mixtures by the broth microdilution method. Analysis of results showed that the acetylated derivatives were the most active of them all.
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Affiliation(s)
- Marta Ferrera-Suanzes
- Department of Organic Chemistry, Faculty of Sciences, Campus Universitario Río San Pedro s/n, Torre Sur, 4; planta, University of Cádiz, 11510 Puerto Real, 11009 Cádiz, Spain; (M.F.-S.); (A.J.M.-O.); (J.M.B.-A.); (R.H.-G.)
| | - Victoria Prieto
- Department of Biomedicine, Biotechnology and Public Health, Hospital Puerta del Mar, University of Cádiz, 11009 Cádiz, Spain; (V.P.); (F.G.-S.); (M.A.R.-I.)
| | - Antonio J. Medina-Olivera
- Department of Organic Chemistry, Faculty of Sciences, Campus Universitario Río San Pedro s/n, Torre Sur, 4; planta, University of Cádiz, 11510 Puerto Real, 11009 Cádiz, Spain; (M.F.-S.); (A.J.M.-O.); (J.M.B.-A.); (R.H.-G.)
| | - José Manuel Botubol-Ares
- Department of Organic Chemistry, Faculty of Sciences, Campus Universitario Río San Pedro s/n, Torre Sur, 4; planta, University of Cádiz, 11510 Puerto Real, 11009 Cádiz, Spain; (M.F.-S.); (A.J.M.-O.); (J.M.B.-A.); (R.H.-G.)
| | - Fátima Galán-Sánchez
- Department of Biomedicine, Biotechnology and Public Health, Hospital Puerta del Mar, University of Cádiz, 11009 Cádiz, Spain; (V.P.); (F.G.-S.); (M.A.R.-I.)
- Instituto de investigación e Innovación Biomédica de Cádiz (INIBICA), 11009 Cádiz, Spain
| | - Manuel A. Rodríguez-Iglesias
- Department of Biomedicine, Biotechnology and Public Health, Hospital Puerta del Mar, University of Cádiz, 11009 Cádiz, Spain; (V.P.); (F.G.-S.); (M.A.R.-I.)
- Instituto de investigación e Innovación Biomédica de Cádiz (INIBICA), 11009 Cádiz, Spain
| | - Rosario Hernández-Galán
- Department of Organic Chemistry, Faculty of Sciences, Campus Universitario Río San Pedro s/n, Torre Sur, 4; planta, University of Cádiz, 11510 Puerto Real, 11009 Cádiz, Spain; (M.F.-S.); (A.J.M.-O.); (J.M.B.-A.); (R.H.-G.)
- Instituto de investigación e Innovación Biomédica de Cádiz (INIBICA), 11009 Cádiz, Spain
| | - María Jesús Durán-Peña
- Department of Organic Chemistry, Faculty of Sciences, Campus Universitario Río San Pedro s/n, Torre Sur, 4; planta, University of Cádiz, 11510 Puerto Real, 11009 Cádiz, Spain; (M.F.-S.); (A.J.M.-O.); (J.M.B.-A.); (R.H.-G.)
- Correspondence: ; Tel.: +34-956-016-583
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